Abstract
The charge-transfer coupling is an important component in tight-binding methods. Because of the highly complex chemical structure of biomolecules, the anisotropic feature of charge-transfer couplings in realistic proteins cannot be ignored. In this work, we have performed the first large-scale quantitative assessment of charge-transfer preference by calculating the charge-transfer couplings in all 20 × 20 possible amino acid side-chain combinations, which are extracted from available high-quality structures of thousands of protein complexes. The charge-transfer database quantitatively shows distinct features of charge-transfer couplings among millions of amino acid side-chain combinations. The overall distribution of charge-transfer couplings reveals that only one average or representative structure cannot be regarded as the typical charge-transfer preference in realistic proteins. This work provides us an alternative route to comprehensively understand the charge-transfer couplings for the overall distribution of realistic proteins in the foreseen big data scenario.
Highlights
Charge transfer is one of the simplest but fundamental reactions in life science.[1−7] Electron- or hole-transfer reactions are possible between donors and acceptors separated by a long distance, that is, across protein−protein complexes.[6,8−13] The charge-transfer effect is suggested to be important to the protein folding or protein−water interactions.[14−16] In biological molecules, the superexchange and hopping mechanisms are commonly used to interpret charge-transfer processes.[5,6,17−19] The tunneling mechanism is a one-step process which exhibits a strong distance dependence, whereas the hopping mechanism provides an explanation for electron or hole transfer across long distances
Bioinformatics scientists have paid much attention to depict the structural significance of these protein complexes, and a large number of biological databases were constructed to classify protein structures in the past decades.[24−31] In addition, the growing amount of high-quality experimental (X-ray, NMR, and cryo-electron microscopy) protein structures have opened space to improve our theoretical understanding of biological charge-transfer reactions
The charge-transfer integrals are calculated for millions of amino acid side-chain combinations to reveal the richness of biological charge-transfer reactions in realistic proteins
Summary
Charge transfer is one of the simplest but fundamental reactions in life science.[1−7] Electron- or hole-transfer reactions are possible between donors and acceptors separated by a long distance, that is, across protein−protein complexes.[6,8−13] The charge-transfer effect is suggested to be important to the protein folding or protein−water interactions.[14−16] In biological molecules, the superexchange (tunneling) and hopping mechanisms are commonly used to interpret charge-transfer processes.[5,6,17−19] The tunneling mechanism is a one-step process which exhibits a strong distance dependence, whereas the hopping mechanism provides an explanation for electron or hole transfer across long distances. The relative abundance of various modes of amino acid contacts (van der Waals contacts and hydrogen bonds) could be completely exploited to understand the nature of electron transfer in proteins. In biomolecule charge-transfer reactions, the charge-transfer rate is proportional to the square of the donor/acceptor electronic coupling strength and the nuclear factor associated with the motion along the reaction coordinate.[6,12,13,37,38] Electronic coupling elements as an important component for biological charge transfer can be Received: February 24, 2018 Accepted: March 30, 2018 Published: April 11, 2018
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